-- Andrej Sali, Ph.D. Professor, Department of Bioengineering and Therapeutic Sciences Director, California Institute for Quantitative Biosciences at UCSF Department of Pharmaceutical Chemistry University of California at San Francisco UCSF MC 2552 Byers Hall Room 503B 1700 4th Street San Francisco, CA 94158-2330, USA Tel +1 (415) 514-4227; Fax +1 (415) 514-4231 Assistant: Ms. Hilary Mahon, hilary@salilab.org, Tel +1 (415)514-4228; Lab +1 (415) 514-4233, 4258 Email sali@salilab.org; Web http://salilab.org Begin forwarded message:

From: "Joy P. Ku" <joyku@stanford.edu> Subject: Rapid MD Prototyping and Simulations on GPU Workshop with Dr. Vijay Pande Date: February 3, 2012 1:19:41 PM PST To: <sali@salilab.org>

Hi Dr. Sali,

I’m the Director of Simbios, an NIH National Center for Biomedical Computing focused on physics-based simulations of biological structures based at Stanford University. Based on your research activities, I thought you would be interested in our upcoming workshop on rapid prototyping and simulations of molecular dynamics on GPUs that we are hosting with Dr. Vijay Pande. Please see the announcement below for the details.

We invite you to attend and would appreciate you forwarding the announcement to colleagues and those in your lab that may be interested.

Thank you.

Regards, Joy Ku On behalf of Vijay Pande and the OpenMM team --------------------------------------------------------------------------------------------------------- Simbios invites you to join us at its next Open Molecular Mechanics (OpenMM) workshop. OpenMM is open-source software that enables molecular dynamics (MD) simulations to be accelerated on high performance computer architectures. It has demonstrated speed ups for both implicit solvent[1] and explicit solvent simulations[2] on graphics processing units (GPUs) [seebenchmarks]. And with the new application layer in its recent release, OpenMM will allow non-programmers to easily and quickly run MD simulations and develop custom algorithms on GPUs, while continuing to enable programmers to integrate OpenMM into their own programs.

***WORKSHOP: RAPID MOLECULAR DYNAMICS PROTOTYPING AND SIMULATIONS ON GPUS ***

Where: Stanford University When: Mar. 12-13, 2012 Description:

During the workshop, you will gain hands-on experience using OpenMM’s new application layer and application programming interface (API). Learn to:

* Set up and run an MD simulation on your GPU using both PDB and AMBER files

* Create a custom force to apply to your simulations

* Customize the simulation through Python scripting

You will also have time to work with the OpenMM development team on your own research project.

This workshop is designed for those interested in accelerating MD simulations on GPUs and/or developing new MD algorithms that can automatically be implemented and accelerated on GPUs. No programming background is required, though programming topics will also be covered for those who are interested in them. Registration:

Registration is free but required and spaces are limited. To register or for more information, visithttp://simbios.stanford.edu/MDWorkshops.htm.

OpenMM is supported by Simbios, an NIH National Center for Physics-Based Simulation of Biological Structures. To learn more about Simbios and its research and software tools, visithttp://simbios.stanford.edu.

[1] OpenMM accelerated code running on NVIDIA GeForce GTX 280 GPU vs. conventional code with Amber9 running on Intel Xenon 2.66 GHz CPU. MS Friedrichs, et al., "Accelerating Molecular Dynamic Simulation on Graphics Processing Units," J. Comp. Chem., 2009, 30(6):864-872. [2]Eastman, P. and Pande, V.S., “Efficient Nonbonded Interactions for Molecular Dynamics on a Graphics Processing Unit,” J. Comp. Chem., 2010, 31(6):1268-1272.